One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/06/peak-motifs.2014-09-06.123915_2014-09-06.123915_sfIm4F/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m4/peak-motifs_oligos_7nt_test_vs_ctrl_m4.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2013-11.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/06/peak-motifs.2014-09-06.123915_2014-09-06.123915_sfIm4F/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m4/peak-motifs_oligos_7nt_test_vs_ctrl_m4_vs_db_jaspar_core_vertebrates

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m4_shift0 ; 4 matrices ; sort_field=rank_mean

Matrix nameAligned logoscor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
oligos_7nt_test_vs_ctrl_m4_shift0 (oligos_7nt_test_vs_ctrl_m4)                                
; oligos_7nt_test_vs_ctrl_m4; m=0 (reference); ncol1=24; shift=0; ncol=24; TmGGkCCAGkCCAAAGwCCAArwk
; Alignment reference
a	0	1	0	0	0	0	0	2	0	0	0	0	2	2	2	0	1	0	0	2	2	1	1	0
c	0	1	0	0	0	2	2	0	0	0	2	2	0	0	0	0	0	2	2	0	0	0	0	0
g	0	0	2	2	1	0	0	0	2	1	0	0	0	0	0	2	0	0	0	0	0	1	0	1
t	2	0	0	0	1	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1
MA0114.1_shift7 (HNF4A) 0.838 0.454 6.625 0.452 0.907 2.909 0.888 1 3 2 2 2 1 1 1.714 1
; oligos_7nt_test_vs_ctrl_m4 versus MA0114.1 (HNF4A); m=1/3; ncol2=13; w=13; offset=7; strand=D; shift=7; score= 1.7143; -------rGgbCAAAGkyCa----
; cor=0.838; Ncor=0.454; logoDP=6.625; NIcor=0.452; NsEucl=0.907; SSD=2.909; NSW=0.888; rcor=1; rNcor=3; rlogoDP=2; rNIcor=2; rNsEucl=2; rSSD=1; rNSW=1; rank_mean=1.714; match_rank=1
a	0	0	0	0	0	0	0	28	2	12	5	3	59	53	56	4	6	3	4	42	0	0	0	0
c	0	0	0	0	0	0	0	7	2	4	23	51	1	2	1	4	2	22	49	7	0	0	0	0
g	0	0	0	0	0	0	0	27	56	35	20	4	3	10	8	58	33	11	5	10	0	0	0	0
t	0	0	0	0	0	0	0	5	7	16	19	9	4	2	2	1	26	31	9	8	0	0	0	0
MA0114.2_rc_shift6 (HNF4A_rc) 0.800 0.500 6.018 0.161 0.908 3.775 0.874 2 1 3 3 1 2 2 2.000 2
; oligos_7nt_test_vs_ctrl_m4 versus MA0114.2_rc (HNF4A_rc); m=2/3; ncol2=15; w=15; offset=6; strand=R; shift=6; score=      2; ------rrGkyCAAAGkyCAg---
; cor=0.800; Ncor=0.500; logoDP=6.018; NIcor=0.161; NsEucl=0.908; SSD=3.775; NSW=0.874; rcor=2; rNcor=1; rlogoDP=3; rNIcor=3; rNsEucl=1; rSSD=2; rNSW=2; rank_mean=2.000; match_rank=2
a	0	0	0	0	0	0	5247	7985	1769	3334	2413	128	16188	13586	15112	49	988	477	70	13410	4057	0	0	0
c	0	0	0	0	0	0	3001	415	352	1662	5340	15741	407	367	0	67	329	8370	15810	907	3974	0	0	0
g	0	0	0	0	0	0	6450	6498	13491	5653	3745	35	173	2637	1630	16535	4425	1846	51	720	5971	0	0	0
t	0	0	0	0	0	0	2070	1870	1156	6119	5270	864	0	178	26	117	11026	6075	837	1731	2766	0	0	0
MA0484.1_shift5 (HNF4G) 0.776 0.485 10.252 0.478 0.904 4.147 0.862 3 2 1 1 3 3 3 2.286 3
; oligos_7nt_test_vs_ctrl_m4 versus MA0484.1 (HNF4G); m=3/3; ncol2=15; w=15; offset=5; strand=D; shift=5; score= 2.2857; -----arrGkyCAAAGkyCA----
; cor=0.776; Ncor=0.485; logoDP=10.252; NIcor=0.478; NsEucl=0.904; SSD=4.147; NSW=0.862; rcor=3; rNcor=2; rlogoDP=1; rNIcor=1; rNsEucl=3; rSSD=3; rNSW=3; rank_mean=2.286; match_rank=3
a	0	0	0	0	0	3514	3259	4696	1103	1944	1511	0	9343	7889	8464	99	324	225	159	6785	0	0	0	0
c	0	0	0	0	0	1864	1531	102	201	713	2870	8827	55	82	0	6	143	4338	8377	794	0	0	0	0
g	0	0	0	0	0	2011	3830	3811	7480	3301	2279	221	54	1481	938	9098	3624	1107	85	556	0	0	0	0
t	0	0	0	0	0	2063	832	843	668	3494	2792	404	0	0	50	249	5361	3782	831	1317	0	0	0	0